Cable cell probing and sampling¶

../_images/probe_sample-diag.svg — A schematic view of how handles let you access sampled data measured at a probeset. A probeset is a probe placed on a locset (which may describe more than one point). When setting a probe on a locset a sampler is created. When this sampler is set to sampling (at a certain schedule), a handle is returned. This figure demonstrates how sampling data can be accessed through the handle associated with the probeset. See below for a possible result for `data`.¶

print(data) # The probe data printed, as found in single_cell_recipe.py
[[ 0.00000000e+00 -4.00000000e+01]
 [ 1.00000000e-01 -5.40211646e+01]
 [ 2.00000000e-01 -6.19670534e+01]
 ...
 [ 2.99000000e+01 -6.44564354e+01]]

Sample data recorded by the Arbor simulation object is returned in the form of a NumPy array, with the first column holding sample times, and subsequent columns holding the corresponding scalar- or vector-valued sample.

Probesets are defined over a location expression and will describe zero, one, or more probes, one per site. They are evaluated in the context of the cell to which the probe is attached.

Vector probes are a kind of probes that samples over a region, rather than a locset. This means that they may output more than a single data point per timestamp. The layout of the outputs as returned by samples() is slightly different, but contains the same sort of information as regular probesets.

../_images/probe_sample_vector-diag.svg — The structure of the data returned is slightly different when a vector probe is sampled. The same kind of information is included however. Instead of returning a list per probe in a probeset, the data and metadata now have an extra dimension to cover for the multitude of subregions.¶

Each of the functions described below generates an opaque probe object for use in the recipe recipe.probes() method.

More information on probes, probe metadata, and sampling can be found in the documentation for the class simulation.

Note

Cable cell probesets are defined analogously to their counterparts in the C++ API (see 5. Probes for details). Some details like \(probe_tag\) are not exposed in Python, as having Python probe callbacks has proven to be too slow.

Example¶

import arbor as A

tree = A.segment_tree()
p = tree.append(A.mnpos, A.mpoint(-3, 0, 0, 3), A.mpoint(3, 0, 0, 3), tag=1)
tree.append(p, A.mpoint(3, 0, 0, 3), A.mpoint(-3, 0, 0, 3), tag=2)
tree.append(p, A.mpoint(3, 0, 0, 3), A.mpoint(-3, 0, 0, 3), tag=2)

decor = (
   A.decor()
   .set_property(Vm=-40)
   .paint('"soma"', A.density("hh"))
   .place('"midpoint"', A.i_clamp(10*U.ms, 2*U.ms, 0.8*U.nA)))

cell = A.cable_cell(tree, decor)

class single_recipe(A.recipe):
   def __init__(self):
      A.recipe.__init__(self)

   def num_cells(self):
      return 1

   def cell_kind(self, gid):
      return A.cell_kind.cable

   def cell_description(self, gid):
      return cell

   def probes(self, gid):
      return [A.cable_probe_membrane_voltage('(location 0 0.5)', tag="Um-soma"),
              A.cable_probe_membrane_voltage_cell(tag="Um-cell"),
              A.cable_probe_membrane_voltage('(join (location 0 0) (location 0 1))', tag="Um-ends"),
               ]

   # Override the global_properties method
   def global_properties(self, kind):
      return A.neuron_cable_properties()

recipe = single_recipe()
sim = A.simulation(recipe)
handles = {tag: sim.sample((0, n), A.regular_schedule(0.1*U.ms))
           for tag in ["Um-soma", "Um-cell", "Um-ends"]}
sim.run(tfinal=1*U.ms)

for tag, hd in handles.items():
   print(f"Handle {hd} Tag '{}'")
   for d, m in sim.samples(hd):
      print(" * Meta:", m)
      print(" * Payload:", d.shape)

This script has a scalar probe, a vector probe, and a probeset involving two scalar probes. The script is complete and can be run with Arbor installed, and will output:

Handle 0 Tag 'Um-soma'
* Meta: (location 0 0.5)
* Payload: (10, 2)
Handle 1 Tag 'Um-cell'
* Meta: [(cable 0 0 1), (cable 0 1 1), (cable 1 0 0), (cable 2 0 0), (cable 1 0 1), (cable 2 0 1)]
* Payload: (10, 7)
Handle 2 Tag 'Um-ends'
* Meta: (location 0 0)
* Payload: (10, 2)
* Meta: (location 0 1)
* Payload: (10, 2)

API¶

class arbor.probe¶

An opaque object that is the Python representation of probe_info.

See below for ways to create probes. In general, all probes are named via the tag argument, as seen above. This tag is later used to retrieve the data collected by the associated probes.

Membrane voltage¶

arbor.cable_probe_membrane_voltage(where, tag)¶

Cell membrane potential (mV) at the sites specified by the location expression string where. This value is spatially interpolated.

Metadata: the explicit location of the sample site.

arbor.cable_probe_membrane_voltage_cell(tag)¶

Cell membrane potential (mV) associated with each cable in each CV of the cell discretization.

Metadata: the list of corresponding cable objects.

Kind: vector probe.

Axial current¶

arbor.cable_probe_axial_current(where, tag)¶

Estimation of intracellular current (nA) in the distal direction at the sites specified by the location expression string where.

Metadata: the explicit location of the sample site.

Ionic current¶

arbor.cable_probe_ion_current_density(where, ion, tag)¶

Transmembrane current density (A/m²) associated with the given ion at sites specified by the location expression string where.

Metadata: the explicit location of the sample site.

arbor.cable_probe_ion_current_cell(ion, tag)¶

Transmembrane current (nA) associated with the given ion across each cable in each CV of the cell discretization.

Metadata: the list of corresponding cable objects.

Kind: vector probe.

Total ionic current¶

arbor.cable_probe_total_ion_current_density(where, tag)¶

Transmembrane current density (A/m²) _excluding_ capacitive currents at the sites specified by the location expression string where.

Metadata: the explicit location of the sample site.

arbor.cable_probe_total_ion_current_cell(tag)¶

Transmembrane current (nA) _excluding_ capacitive currents across each cable in each CV of the cell discretization. Stimulus currents are not included.

Metadata: the list of corresponding cable objects.

Kind: vector probe.

Total transmembrane current¶

arbor.cable_probe_total_current_cell(tag)¶

Transmembrane current (nA) including capacitive currents across each cable in each CV of the cell discretization. Stimulus currents are not included.

Metadata: the list of corresponding cable objects.

Kind: vector probe.

Total stimulus current¶

arbor.cable_probe_stimulus_current_cell(tag)¶

Total stimulus current (nA) across each cable in each CV of the cell discretization.

Metadata: the list of corresponding cable objects.

Kind: vector probe.

Density mechanism state variable¶

arbor.cable_probe_density_state(where, mechanism, state, tag)¶

The value of the state variable state in the density mechanism mechanism at the sites specified by the location expression where.

Metadata: the explicit location of the sample site.

arbor.cable_probe_density_state_cell(mechanism, state, tag)¶

The value of the state variable state in the density mechanism mechanism on each cable in each CV of the cell discretization.

Metadata: the list of corresponding cable objects.

Kind: vector probe.

Point process state variable¶

arbor.cable_probe_point_state(target, mechanism, state, tag)¶

The value of the state variable state in the point process mechanism associated with the target index target on the cell. If the given mechanism is not associated with the target index, no probe will be generated.

Metadata:

class arbor.cable_point_probe_info¶

target¶

tag of target mechanism on the cell

lid¶

local id of target;

multiplicity¶

number of targets sharing the same state in the discretization;

location¶

location object corresponding to the target site.

arbor.cable_probe_point_state_cell(mechanism, state, tag)¶

The value of the state variable state in the point process mechanism at each of the targets where that mechanism is defined.

Metadata: a list of cable_point_probe_info values, one for each matching target.

Kind: vector probe.

Ionic internal concentration¶

arbor.cable_probe_ion_int_concentration(where, ion, tag)¶

Ionic internal concentration (mmol/L) of the given ion at the sites specified by the location expression string where.

Metadata: the explicit location of the sample site.

arbor.cable_probe_ion_int_concentration_cell(ion, tag)¶

Ionic internal concentration (mmol/L) of the given ion in each cable in each CV of the cell discretization.

Metadata: the list of corresponding cable objects.

Kind: vector probe.

Ionic external concentration¶

arbor.cable_probe_ion_ext_concentration(where, ion, tag)¶

Ionic external concentration (mM) of the given ion at the sites specified by the location expression string where.

Metadata: the explicit location of the sample site.

arbor.cable_probe_ion_ext_concentration_cell(ion, tag)¶

Ionic external concentration (mmol/L) of the given ion in each able in each CV of the cell discretization.

Metadata: the list of corresponding cable objects.

Kind: vector probe.

Ionic diffusion concrentration¶

arbor.cable_probe_ion_diff_concentration_cell(ion, tag)¶

Diffusive ionic concentration of the given ion for each cable in each CV.

Metadata: the explicit location of the sample site.

Kind: vector probe.

arbor.cable_probe_ion_diff_concentration(where, ion, tag)¶

Diffusive ionic concentration of the given ion at the sites specified by the location expression string where.

Metadata: the list of corresponding cable objects.

Reversal potential¶

arbor.cable_probe_ion_reversal_potential_cell(ion, tag)¶

Reversal potential of the given ion for each cable in each CV.

Metadata: the explicit location of the sample site.

Kind: vector probe.

arbor.cable_probe_ion_reversal_potential(where, ion, tag)¶

Reversal potential of the given ion at the sites specified by the location expression string where.

Metadata: the list of corresponding cable objects.

LIF Cell probing¶

Membrane voltage¶

arbor.lif_probe_voltage(tag)¶

Current cell membrane potential (mV).

Metadata: none

AdEx cell probing and sampling¶

Membrane voltage¶

arbor.adex_probe_voltage()¶

Queries cell membrane potential.

Sample value: double. Membrane potential (mV).
Metadata: none

Adaption Variable¶

arbor.adex_probe_adaption()¶

Queries cell adaption variable \(w\).

Sample value: double. (nA).
Metadata: none